Placing his hand on a Bible, wearing the gold shoulder boards that had been pinned on him moments before, Rear Adm. James A. Helis looked out at several hundred uniformed students last month and took the oath of office as the new leader of the United States Merchant Marine Academy. He was the fourth person to do so in the last four years.

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Niko J. Kallianiotis for The New York Times
Colonel Helis, center, took his oath of office at the ceremony in Kings Point, N.Y., on July 30. He is the marine academy’s fourth leader in four years.
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Niko J. Kallianiotis for The New York Times
A midshipman en route to the cafeteria at the Merchant Marine Academy, where the food has been ranked the seventh worst, according to a Princeton Review survey of colleges nationwide.
Over that period, the school — the least well known of the nation’s five service academies, despite its location just outside New York City — has been in a state of turmoil that includes financial disarray, deteriorating facilities and extreme student dissatisfaction. In January, a carbon monoxide leak sent three dozen people to the hospital. Last year, federal investigators spent time on campus looking into allegations that two administrators had been fraternizing with students after hours.

Ray LaHood, the federal transportation secretary whose department oversees the academy, has won a record $85 million annual budget for it and vowed to help it right its course. But given the cost, the state of affairs and an American maritime industry that has shifted away from the academy’s traditional curriculum, some loudly question whether the academy is still relevant.

“It’s an educational institution for an age that the U.S. doesn’t participate in any more,” said Capt. John Konrad, the editor of gCaptain, a blog widely read in the maritime industry.

The Merchant Marine Academy is an anomaly: the only national service academy that is not a part of the military. Over the course of a grueling four-year program that includes at least 300 days at sea, it trains about 1,000 undergraduates free of tuition to become officers in the United States’ commercial shipping industry. They graduate with a Bachelor of Science degree, a Coast Guard license, an expectation of five years’ service in some maritime capacity, and — for those who do not pursue active military duty — a spot in the Navy Reserve.

The academy was founded to support American shipping and to enhance national security. But on gCaptain’s numerous discussion groups devoted to the school, contributors routinely call for the federal government to leave the training of merchant mariners to state academies (including the State University of New York Maritime College, in the Bronx, a boat ride of about a mile and a half from the federal academy’s campus, near Great Neck) or to the industry itself.

Mr. LaHood waved away the suggestion that the academy represents any disproportionate government subsidy. “It’s no different from what we would offer to other industries that are involved in transportation,” he says, citing taxpayer support of Amtrak, or federal jurisdiction over the airline industry.

Splendidly situated on Long Island Sound, in the village of Kings Point, the academy has a proud and patriotic history. During World War II, 142 of the school’s students died on active duty. On Sept. 11, 2001, Kings Pointers were among the first to arrive at the mouth of the Hudson River. The school’s main administrative building, Wiley Hall, was once the Chrysler mansion; all around it, immaculately attired students — or midshipmen, as they are locally known — scurry from academic classes to technical training to regimental duties to athletic practice.

Speaking in the company of a Transportation Department press officer, one senior, Steven Webb, said life at Kings Point had “far exceeded” his expectations, and called the sea year “a very valuable life experience.” But in the most recent Princeton Review survey of American colleges, the academy was No. 4 nationwide in the category of “Least Happy Students.” (It came in third for “Professors Get Low Marks,” and seventh for “Is It Food?”)

And in an unchaperoned conversation, a couple dozen of Mr. Webb’s peers complained about a dearth of recreational activities, an out-of-date curriculum, a regimental system that does not reward leadership, and facilities — including barracks that have no air conditioning and an empty stretch of dock where the school’s training vessel used to be — that are in demoralizingly poor condition. The carbon monoxide leak occurred in one of those barracks.

In 2009 the Government Accountability Office found “numerous instances of improper and questionable sources and uses of funds” and “numerous breakdowns in its important stewardship responsibilities,” including “a lack of awareness or support for strong internal control and accountability across the Academy at all levels and risks.” In 2010, a dire report by the Transportation Department warned that failing to upgrade the school’s facilities — which would require spending hundreds of millions of dollars — “will result in the decline of the institution and risks the eventual loss of the school’s accreditation.”

Amid all these challenges, Admiral Helis is in one way an unlikely savior: he has no maritime training. But he is a decorated veteran, a retired colonel whose 30 years of Army service took him from Haiti to Sweden to Afghanistan, as well as an accomplished scholar with a Ph.D. in international relations from Tufts University and two master’s degrees. Since 2004 he had taught at the United States Army War College in Pennsylvania, where he led its Department of National Security and Strategy.

In an interview, Admiral Helis seemed calm and confident. “I see this as a great opportunity,” he said. “We have a Secretary and the Department of Transportation that are passionately committed to this institution and its future. We’ve seen significant infusion of resources. I see the future as very bright for the academy.”

He declined to comment on anything that preceded his tenure, including the allegations of improper contact between administrators and students. Some of those who were interviewed by Transportation Department investigators last year, but who asked not to be identified because the department has not authorized them to speak about it, said the investigation centered on allegations that two administrators threw parties in their on-campus residences, served alcohol to underage students and kept them out after their curfew.

“We take any allegation of misconduct by an academy staff member very seriously,” said Sasha Johnson, a spokeswoman for the Transportation Department. But she said no evidence was found to substantiate the accusations and “no charges — criminal or otherwise — were ever brought.” The two administrators were later transferred to Transportation Department jobs outside New York, but Ms. Johnson said the moves were unrelated to the investigation. “Several academy employees have left over the past year for other assignments as the academy has realigned staff and priorities,” she said.

Admiral Helis’s first weeks on campus have been eventful. A few days after his installation ceremony, he unveiled a new strategic planning report that was several months in the making and several years overdue. He met with faculty and staff and began trying to address the most egregious aspects of student dissatisfaction. And he got his first glimpse of what his son Ian, a first-year “plebe candidate” (who had been accepted to Kings Point before his father had his first interview for the job), looked like with a shaved head.

Merely having a leader who will last more than a year or two, several students and staff members said, could do a lot to improve morale. But in addition to the challenges on campus, Admiral Helis must navigate a maritime industry that has changed greatly since the era of the school’s founding. Back then, American ships were a major presence in intercontinental shipping routes. Today that “blue-water” business is largely the domain of foreign ships, which do the job for less.

The American maritime industry has found new opportunities in “brown-water” shipping — along coast lines, in rivers and in the Great Lakes — and in offshore drilling. With a rapidly aging work force, job opportunities abound. But critics say the school has not adapted to those new opportunities. Its curriculum, Captain Konrad said, “is not focused on the new age of technologically advanced offshore rigs, sub-sea engineering and development of new ideas for port structures and systems.”

Sean T. Connaughton, a former head of the Maritime Administration, the Transportation Department agency that oversees the school, views the matter differently. “They’re correct that the training curriculum is still geared toward the blue water,” he said, “but, at the end of the day, that’s because the licensing standards are so strict that they have to do that to end up with the highest class of license that they’re eligible for.”

Admiral Helis says the training that midshipmen receive is under review. “Part of the strategic plan,” he said, “was reaching out to stakeholders in the maritime industry: what are the skill sets, what is the knowledge they need, so we can infuse that into the curriculum.”

The G.A.O. said in a follow-up to its 2009 report that the school had addressed many of its concerns, and Admiral Helis said reorganization would address the rest of them.

Meanwhile, the shuttered student recreation center is scheduled to reopen in September. The crumbling pier is soon to be replaced. Student barracks are slated to get air conditioning. And the school has recently signed a contract for a new training vessel.

Capt. John C. Kennedy, the school’s commandant of midshipmen, said the mood was changing, even for the least happy students. “There was a certain amount of cynicism when I arrived,” he said. “This is a hard place. But now I think they are cautiously optimistic about the future here.”